tripal/tripal_pub/tripal_pub.module

<?php
/**
 * @file
 * Basic functionality of the pub module
 */

require_once 'api/tripal_pub.api.inc';
require_once 'api/tripal_pub.DEPRECATED.inc';

require_once 'theme/tripal_pub.theme.inc';

require_once 'includes/tripal_pub.admin.inc';
require_once 'includes/tripal_pub.chado_node.inc';
require_once 'includes/tripal_pub.pub_importers.inc';
require_once 'includes/tripal_pub.pub_search.inc';
require_once 'includes/tripal_pub.pub_citation.inc';
require_once 'includes/importers/tripal_pub.PMID.inc';
require_once 'includes/importers/tripal_pub.AGL.inc';

/**
 * @defgroup tripal_pub Publication Module
 * @ingroup tripal_modules
 * @{
 * Integrates the Chado Publication module with Drupal Nodes & Views, as well as, provides
 * the ability to import publication from PubMed
 *
 * The Tripal Publication module allows you to search the PubMed database for academic articles,
 * that relate to user specified topic\s. As well, it allows management of publications so that
 * a user can enter specified details regarding a desired publication. This allows all of the important
 * information that is unique to a Academic Publication to be stored for access.
 * @}
 */

/**
 * Implements hook_menu().
 *
 * Adds menu items for the tripal_pub module menu. This section
 * gives the outline for the main menu of the Tripal-Publication module
 *
 * @return
 *   An array of menu items that is visible within the Drupal Menu, returned as soon
 *   as the program is ran
 *
 * @ingroup tripal_pub
 */
function tripal_pub_menu() {
  $items = array();

  // because the publication search is not views we need to manually add
  // it to the Search Data list in the navigation menu
  $items['chado/publication' ]= array(
    'title' => 'Publications',
    'description' => ('Publications such as journal articles, conference proceedings, or other media.'),
    'page callback' => 'tripal_pub_search_page',
    'access arguments' => array('access chado_pub content'),
    'type' => MENU_NORMAL_ITEM
  );

  // for backwards compatibility the same chado/publications is also found
  // at find/publications
  $items['find/publications' ]= array(
    'title' => 'Publication Search',
    'description' => ('Search for publications'),
    'page callback' => 'tripal_pub_search_page',
    'access arguments' => array('access chado_pub content'),
    'type' => MENU_CALLBACK
  );
  


  $items['find/publications/criteria/%/%'] = array(
    'page callback' => 'tripal_pub_search_page_update_criteria',
    'page arguments' => array(5, 6),
    'access arguments' => array('access chado_pub content'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_pub']= array(
    'title' => 'Publications',
    'description' => ('A documented provenance artefact - publications, documents, personal communication.'),
    'page callback' => 'tripal_pub_admin_pub_view',
    'access arguments' => array('administer tripal pub'),
    'type' => MENU_NORMAL_ITEM
  );

  $items['admin/tripal/chado/tripal_pub/help']= array(
    'title' => 'Help',
    'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_pub_help'),
    'access arguments' => array('administer tripal pub'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );

  $items['admin/tripal/chado/tripal_pub/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Configure the Tripal publication module.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_pub_admin'),
    'access arguments' => array('administer tripal pub'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );

  $items['admin/tripal/chado/tripal_pub/sync'] = array(
    'title' => ' Sync',
    'description' => 'Create pages on this site for libraries stored in Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('chado_node_sync_form', 'tripal_pub', 'chado_pub'),
    'access arguments' => array('administer tripal pub'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2
  );

  $items['admin/tripal/chado/tripal_pub/citation'] = array(
    'title' => 'Citations',
    'description' => 'Update publication citations',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_pub_citation_form'),
    'access arguments' => array('administer tripal pub'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 1
  );

  $items['admin/tripal/chado/tripal_pub/import_list'] = array(
    'title' => t('Publication Importers'),
    'description' => t('Create and modify importers that can connect to and retreive publications from remote databases.'),
    'page callback' => 'tripal_pub_importers_list',
    'access arguments' => array('administer tripal pub'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 0
  );

  // add a second link for the importer on the data loaders page
  $items['admin/tripal/loaders/pub_import'] = array(
    'title' => t('Publication Importers'),
    'description' => t('Create and modify importers that can connect to and retreive publications from remote databases.'),
    'page callback' => 'tripal_pub_importers_list',
    'access arguments' => array('administer tripal pub'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/chado/tripal_pub/import/new'] = array(
    'title' => t('Add an Importer'),
    'description' => t('Add a new publication importer.'),
    'page callback' => 'tripal_pub_importer_setup_page',
    'access arguments' => array('administer tripal pub'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_pub/import/raw/%'] = array(
    'title' => t('Raw Data From Publication Import'),
    'page callback' => 'tripal_get_remote_pub_raw_page',
    'page arguments' => array(6),
    'access arguments' => array('administer tripal pub'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_pub/import/edit/%'] = array(
    'page callback' => 'tripal_pub_importer_setup_page',
    'page arguments' => array(5, 6),
    'access arguments' => array('administer tripal pub'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_pub/import/submit/%'] = array(
    'page callback' => 'tripal_pub_importer_submit_job',
    'page arguments' => array(6),
    'access arguments' => array('administer tripal pub'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_pub/import/delete/%'] = array(
    'page callback' => 'tripal_pub_importer_delete',
    'page arguments' => array(5),
    'access arguments' => array('administer tripal pub'),
    'type ' => MENU_CALLBACK,
  );
  $items['admin/tripal/chado/tripal_pub/import/changedb'] = array(
    'page callback' => 'tripal_pub_importer_setup_page_update_remotedb',
    'page arguments' => array(),
    'access arguments' => array('administer tripal pub'),
    'type ' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_pub/import/criteria/%/%'] = array(
    'page callback' => 'tripal_pub_importer_setup_page_update_criteria',
    'page arguments' => array(5, 6),
    'access arguments' => array('administer tripal pub'),
    'type ' => MENU_CALLBACK,
  );

  return $items;
}

/**
 * Implements hook_theme().
 * Register themeing functions for this module
 *
 * @return
 *   An array of themeing functions to register
 *
 * @ingroup tripal_pub
 */
function tripal_pub_theme($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');

  $items = array(
    'node__chado_pub' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme/templates",
    ),
    // node templates
    'tripal_pub_authors' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_authors',
      'path' => "$path/theme/templates",
    ),
    'tripal_pub_base' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_base',
      'path' => "$path/theme/templates",
    ),
    'tripal_pub_featuremaps' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_featuremaps',
      'path' => "$path/theme/templates",
    ),
    'tripal_pub_features' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_features',
      'path' => "$path/theme/templates",
    ),
    'tripal_pub_libraries' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_libraries',
      'path' => "$path/theme/templates",
    ),
    'tripal_pub_projects' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_projects',
      'path' => "$path/theme/templates",
    ),
    'tripal_pub_properties' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_properties',
      'path' => "$path/theme/templates",
    ),
    'tripal_pub_references' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_references',
      'path' => "$path/theme/templates",
    ),
    'tripal_pub_relationships' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_relationships',
      'path' => "$path/theme/templates",
    ),
    'tripal_pub_stocks' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_pub_stocks',
      'path' => "$path/theme/templates",
    ),

    // instructions page for the pub module
    'tripal_pub_help' => array(
      'template' => 'tripal_pub_help',
      'arguments' =>  array(NULL),
      'path' => "$path/theme/templates",
    ),

    // themed forms
    'tripal_pub_importer_setup_form_elements' => array(
      'render element' => 'form',
    ),
    'tripal_pub_search_setup_form_elements' => array(
      'render element' => 'form',
    ),

    // teaser
    'tripal_pub_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_pub_teaser',
      'path' => "$path/theme/templates",
    ),
  );

  return $items;
}

/**
 * Implements hook_help().
 * Adds a help page to the module list
 *
 * @ingroup tripal_pub
 */
function tripal_pub_help ($path, $arg) {
  if ($path == 'admin/help#tripal_pub') {
    return theme('tripal_pub_help', array());
  }
}

/**
 * Implements hook_views_api().
 *
 * Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_db.views.inc where all the
 *  views integration code is
 *
 * @ingroup tripal_pub
 */
function tripal_pub_views_api() {
  return array(
    'api' => 3.0,
  );
}

/**
 * Implement hook_permission().
 *
 * @ingroup tripal_pub
 */
function tripal_pub_permission() {
  return array(
    'access chado_pub content' => array(
      'title' => t('View Publications'),
      'description' => t('Allow users to view publication pages.'),
    ),
    'create chado_pub content' => array(
      'title' => t('Create Publication'),
      'description' => t('Allow users to create new publication pages.'),
    ),
    'delete chado_pub content' => array(
      'title' => t('Delete Publication'),
      'description' => t('Allow users to delete publication pages.'),
    ),
    'edit chado_pub content' => array(
      'title' => t('Edit Publications'),
      'description' => t('Allow users to edit publication pages.'),
    ),
    'administer tripal pub' => array(
      'title' => t('Administer Publications'),
      'description' => t('Allow users to administer all publications.'),
    ),
  );
}

/**
 * Implements hook_mail().
 *
 * @ingroup tripal_pub
 */
function tripal_pub_mail($key, &$message, $params) {
  $language = $message['language'];
  $variables = user_mail_tokens($params['account'], $language);
  switch($key) {
    case 'import_report':
      $headers = array(
        'MIME-Version' => '1.0',
        'Content-Type' => 'text/html; charset=UTF-8; format=flowed',
        'Content-Transfer-Encoding' => '8Bit',
        'X-Mailer' => 'Drupal'
        );
        foreach ($headers as $key => $value) {
          $message['headers'][$key] = $value;
        }
        $message['subject'] = t('Publication import from !site', $variables, $language->language);
        $message['body'][] = $params['message'];
        break;
  }
}

/**
 * Implementation of hook_form_alter().
 *
 * @param $form
 * @param $form_state
 * @param $form_id
 *
 * @ingroup tripal_pub
 */
function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
  // turn of preview button for insert/updates
  if ($form_id == "chado_pub_node_form") {
    // turn of preview button for insert/updates
    $form['actions']['preview']['#access'] = FALSE;
    
    //remove the body field
    unset($form['body']);
  }
  if ($form_id == "tripal_pub_importer_setup_form") {
/*    // updating the form through the ahah callback sets the action of
    // the form to the ahah callback URL. We need to set it back
    // to the normal form URL
    if (array_key_exists('values', $form_state) and $form_state['values']['action'] == 'edit') {
      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/edit/" . $form_state['values']['pub_import_id']);
    }
    if (array_key_exists('values', $form_state) and $form_state['values']['action'] == 'new') {
      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/new");
    }
    */
  }
  if ($form_id == "tripal_pub_search_form") {
    $form['#action'] = url("find/publications");
  }
  if ($form_id == "chado_pub_node_form") {
  }
}

/**
 * Implements hook_job_describe_args().
 *
 * @param $callback
 * @param $args
 *
 * @ingroup tripal_pub
 */
function tripal_pub_job_describe_args($callback, $args) {

  $new_args = array();
  if ($callback == 'tripal_execute_pub_importer') {
    // get all of the loaders
    $qargs = array(':import_id' => $args[0]);
    $sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = :import_id ";
    $import = db_query($sql, $qargs)->fetchObject();

    $new_args['Importer'] = $import->name;
  }
  return $new_args;
}


/** 
 * A simple wrapper function to put <pre> tags around the raw results
 * returned by the 
 * @param unknown $dbxref
 * @return string
 */
function tripal_get_remote_pub_raw_page($dbxref) {
  $pub = tripal_get_remote_pub($dbxref);
  if ($pub) {
    $page = "<strong>Raw results for $dbxref:</strong><br><br>";
    $page.= '<textarea cols=80 rows=20>' . $pub['raw'] . '</textarea>';
    return $page;
  }
  return "Cound not find the requested publication ($dbxref)";
}

/**
 * 
 */
function tripal_pub_search_biological_data_views() {
  return array(
    'publications' => array(
      'machine_name' => 'publications',
      'human_name'   => 'Publications',
      'description'  => 'Publications such as journal articles, conference proceedings, or other media.',
      'link'         => 'find/publications'
    ),
  );
}